3h16 - Revision history

OCA at 09:57, 21 February 2024

2024-02-21T09:57:47Z

←Older revision		Revision as of 09:57, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3h16' size='340' side='right'caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3h16' size='340' side='right'caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pardp Pardp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H16 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Pden_0113, PdTLP ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [https://pdbe.org/3h16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [https://www.ebi.ac.uk/pdbsum/3h16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h16 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [https://pdbe.org/3h16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [https://www.ebi.ac.uk/pdbsum/3h16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h16 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PDTIR_PARDP PDTIR_PARDP] NAD(+) hydrolase (NADase) that catalyzes cleavage of NAD(+) into ADP-D-ribose (ADPR) and nicotinamide.<ref>PMID:29395922</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3h16 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3h16 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Macrophages detect pathogen infection via the activation of their plasma membrane-bound Toll-like receptor proteins (TLRs). The heterotypic interaction between the Toll/interleukin-1 receptor (TIR) domains of TLRs and adaptor proteins, like Myeloid differentiation primary response gene 88 (MyD88), is the first intracellular step in the signaling pathway of the mammalian innate immune response. The hetero-oligomerization of the TIRs of the receptor and adaptor brings about the activation of the transcription factor NF-kappaB, which regulates the synthesis of pro-inflammatory cytokines. Here, we report the first crystal structure of a bacterial TIR domain solved at 2.5 A resolution. The three-dimensional fold of Paracoccus denitrificans TIR is identical to that observed for the TIR of human TLRs and MyD88 proteins. The structure shows a unique dimerization interface involving the DD-loop and EE-loop residues, whereas leaving the BB-loop highly exposed. Peptide amide hydrogen-deuterium exchange mass spectrometry also reveals that the same region is used for dimerization in solution and in the context of the full-length protein. These results, together with a functional interaction between P. denitrificans TIR and MyD88 visualized in a co-immunoprecipitation assay, further substantiate the model that bacterial TIR proteins adopt structural mimicry of the host active receptor TIR domains to interfere with the signaling of TLRs and their adaptors to decrease the inflammatory response.
-
-	Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain.,Chan SL, Low LY, Hsu S, Li S, Liu T, Santelli E, Le Negrate G, Reed JC, Woods VL Jr, Pascual J J Biol Chem. 2009 Aug 7;284(32):21386-92. Epub 2009 Jun 17. PMID:19535337<ref>PMID:19535337</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3h16" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pardp~~]]	+	[[Category: Paracoccus denitrificans PD1222]]
-	[[Category: Chan~~, S L~~]]	+	[[Category: Chan SL]]
-	[[Category: Low~~, L Y~~]]	+	[[Category: Low LY]]
-	[[Category: Pascual, J]]	+	[[Category: Pascual J]]
-	[[Category: Santelli, E]]	+	[[Category: Santelli E]]
-	~~[[Category: Bacteria tir domain]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 08:00, 16 March 2022

2022-03-16T08:00:18Z

←Older revision		Revision as of 08:00, 16 March 2022
Line 1:		Line 1:

	==Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans==		==Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans==
-	<StructureSection load='3h16' size='340' side='right' caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='3h16' size='340' side='right'caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3H16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H16 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [~~http~~://pdbe.org/3h16 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3h16 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3h16 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [https://pdbe.org/3h16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [https://www.ebi.ac.uk/pdbsum/3h16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h16 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/3h16_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/3h16_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pardp]]		[[Category: Pardp]]
	[[Category: Chan, S L]]		[[Category: Chan, S L]]

OCA at 07:18, 1 November 2017

2017-11-01T07:18:32Z

←Older revision		Revision as of 07:18, 1 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans==		==Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans==
	<StructureSection load='3h16' size='340' side='right' caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3h16' size='340' side='right' caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [http://pdbe.org/3h16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [http://www.ebi.ac.uk/pdbsum/3h16 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [http://pdbe.org/3h16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [http://www.ebi.ac.uk/pdbsum/3h16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3h16 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 18:36, 9 February 2016

2016-02-09T18:36:59Z

←Older revision		Revision as of 18:36, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3h16' size='340' side='right' caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3h16' size='340' side='right' caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H16 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 ~~Paracoccus denitrificans PD1222~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [http://www.ebi.ac.uk/pdbsum/3h16 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [http://pdbe.org/3h16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [http://www.ebi.ac.uk/pdbsum/3h16 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3h16 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3h16" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Paracoccus denitrificans pd1222~~]]	+	[[Category: Pardp]]
	[[Category: Chan, S L]]		[[Category: Chan, S L]]
	[[Category: Low, L Y]]		[[Category: Low, L Y]]

OCA at 08:59, 8 December 2014

2014-12-08T08:59:43Z

←Older revision		Revision as of 08:59, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3h16.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans==
		+	<StructureSection load='3h16' size='340' side='right' caption='[[3h16]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3h16]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H16 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_0113, PdTLP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 Paracoccus denitrificans PD1222])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3h16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h16 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3h16 RCSB], [http://www.ebi.ac.uk/pdbsum/3h16 PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/3h16_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Macrophages detect pathogen infection via the activation of their plasma membrane-bound Toll-like receptor proteins (TLRs). The heterotypic interaction between the Toll/interleukin-1 receptor (TIR) domains of TLRs and adaptor proteins, like Myeloid differentiation primary response gene 88 (MyD88), is the first intracellular step in the signaling pathway of the mammalian innate immune response. The hetero-oligomerization of the TIRs of the receptor and adaptor brings about the activation of the transcription factor NF-kappaB, which regulates the synthesis of pro-inflammatory cytokines. Here, we report the first crystal structure of a bacterial TIR domain solved at 2.5 A resolution. The three-dimensional fold of Paracoccus denitrificans TIR is identical to that observed for the TIR of human TLRs and MyD88 proteins. The structure shows a unique dimerization interface involving the DD-loop and EE-loop residues, whereas leaving the BB-loop highly exposed. Peptide amide hydrogen-deuterium exchange mass spectrometry also reveals that the same region is used for dimerization in solution and in the context of the full-length protein. These results, together with a functional interaction between P. denitrificans TIR and MyD88 visualized in a co-immunoprecipitation assay, further substantiate the model that bacterial TIR proteins adopt structural mimicry of the host active receptor TIR domains to interfere with the signaling of TLRs and their adaptors to decrease the inflammatory response.

-	~~{{STRUCTURE_3h16\| PDB=3h16 \| SCENE= }}~~	+	Molecular mimicry in innate immunity: crystal structure of a bacterial TIR domain.,Chan SL, Low LY, Hsu S, Li S, Liu T, Santelli E, Le Negrate G, Reed JC, Woods VL Jr, Pascual J J Biol Chem. 2009 Aug 7;284(32):21386-92. Epub 2009 Jun 17. PMID:19535337<ref>PMID:19535337</ref>

-	~~===Crystal structure of a bacteria TIR domain~~, ~~PdTIR from Paracoccus denitrificans===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19535337}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3h16]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019535337<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Paracoccus denitrificans pd1222]]		[[Category: Paracoccus denitrificans pd1222]]
-	[[Category: Chan, S L.]]	+	[[Category: Chan, S L]]
-	[[Category: Low, L Y.]]	+	[[Category: Low, L Y]]
-	[[Category: Pascual, J.]]	+	[[Category: Pascual, J]]
-	[[Category: Santelli, E.]]	+	[[Category: Santelli, E]]
	[[Category: Bacteria tir domain]]		[[Category: Bacteria tir domain]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

OCA: Protected "3h16" [edit=sysop:move=sysop]

2013-02-27T15:32:14Z

Protected "3h16" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:32, 27 February 2013

OCA at 15:32, 27 February 2013

2013-02-27T15:32:12Z

←Older revision		Revision as of 15:32, 27 February 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3h16.png\|left\|200px]]		[[Image:3h16.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3h16", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3h16\| PDB=3h16 \| SCENE= }}		{{STRUCTURE_3h16\| PDB=3h16 \| SCENE= }}

	===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===		===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===

		+	{{ABSTRACT_PUBMED_19535337}}

	==About this Structure==		==About this Structure==
-	~~3H16~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].	+	[[3h16]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019535337</ref><references group="xtra"/>
	[[Category: Paracoccus denitrificans pd1222]]		[[Category: Paracoccus denitrificans pd1222]]
	[[Category: Chan, S L.]]		[[Category: Chan, S L.]]
Line 22:		Line 19:
	[[Category: Bacteria tir domain]]		[[Category: Bacteria tir domain]]
	[[Category: Signaling protein]]		[[Category: Signaling protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 19 20:10:00 2009''

OCA at 17:03, 19 August 2009

2009-08-19T17:03:28Z

←Older revision		Revision as of 17:03, 19 August 2009
Line 12:		Line 12:
	===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===		===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19535337}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19535337 is the PubMed ID number.
-	-->
-	{{ABSTRACT_PUBMED_19535337}}

	==About this Structure==		==About this Structure==
	3H16 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].		3H16 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].
-
-	==Reference==
-	<ref group="xtra">PMID:19535337</ref><references group="xtra"/>
	[[Category: Paracoccus denitrificans pd1222]]		[[Category: Paracoccus denitrificans pd1222]]
	[[Category: Chan, S L.]]		[[Category: Chan, S L.]]
Line 32:		Line 23:
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 19 12:56:13 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 19 20:10:00 2009''

OCA at 09:56, 19 August 2009

2009-08-19T09:56:17Z

←Older revision		Revision as of 09:56, 19 August 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3h16.~~jpg~~\|left\|200px]]	+	[[Image:3h16.png\|left\|200px]]

	<!--		<!--
Line 12:		Line 12:
	===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===		===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19535337}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19535337 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19535337}}

	==About this Structure==		==About this Structure==
	3H16 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].		3H16 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19535337</ref><references group="xtra"/>
	[[Category: Paracoccus denitrificans pd1222]]		[[Category: Paracoccus denitrificans pd1222]]
	[[Category: Chan, S L.]]		[[Category: Chan, S L.]]
Line 23:		Line 32:
	[[Category: Signaling protein]]		[[Category: Signaling protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 17 11~~:31:06 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 19 12:56:13 2009''

OCA at 08:31, 17 June 2009

2009-06-17T08:31:08Z

←Older revision		Revision as of 08:31, 17 June 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3h16.jpg\|left\|200px]]

-	The ~~entry 3h16~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3h16", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3h16\| PDB=3h16 \| SCENE= }}

-	~~Authors: Chan~~, ~~S.L., Low, L.Y., Santelli, E., Pascual, J.~~	+	===Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans===

-	Description: Crystal structure of a bacteria TIR domain, PdTIR from Paracoccus denitrificans

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 22~~ 11:09:39 2009''	+	==About this Structure==
		+	3H16 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H16 OCA].
		+	[[Category: Paracoccus denitrificans pd1222]]
		+	[[Category: Chan, S L.]]
		+	[[Category: Low, L Y.]]
		+	[[Category: Pascual, J.]]
		+	[[Category: Santelli, E.]]
		+	[[Category: Bacteria tir domain]]
		+	[[Category: Signaling protein]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 17 11:31:06 2009''